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Haplotype caller-generated VCF cannot be validated
Hi, I have VCFs generated by Haplotype Caller and Unified Genotyper on the NA12878 genome. Running Variant Recalibrator brings up errors in the VCF, so I'm attempting to understand them using GATK Validate Variants.
Should the Validate Variants tool run through a Haplotype caller-generated VCF no problem? It's fine with the Unified Genotyper VCF, but the Haplotype Caller VCF returns a number of errors. Specifically:
ERROR MESSAGE: File /home/felix/Genomics/VCFs/HCoutput1.vcf fails strict validation: one or more of the ALT allele(s) for the record at position 1:825826 are not observed at all in the sample genotypes,
Then if I rerun with --validationTypeToExclude ALLELES, I get:
ERROR MESSAGE: File /home/felix/Genomics/VCFs/HCoutput1.vcf fails strict validation: the Allele Number (AN) tag is incorrect for the record at position 1:825826, 2 vs. 0
I'm not sure how this has come about, because the Unified Genotyper-generated VCF on the exact same input BAM has no errors.
Any pointers would be greatly appreciated.